Tired of waiting for results from slow BLAST* processes?
Using BLAST on large data sets may - even with powerful computers result in processing times that run into many hours, days or even weeks!.
OfficeGRID BLAST from MESH-Technologies is an improved version of NCBI BLAST, that speeds up BLAST processing dramatically and delivers results much faster. As an added benefit, OfficeGRID BLAST can run on traditional Linux cluster computers, standard Windows computers or a combination of both!
This way you can increase your computational power dynamically at very low cost, and even allow standard office PCs to participate in BLAST processing when they otherwise are not used.
OfficeGRID BLAST from MESH-Technologies is a parallellization of NCBI BLAST, which is developed by the U.S. National Center for Biotechnology Information.
OfficeGRID BLAST runs on OfficeGRID from MESH-Technologies which allows for the combination of Linux clusters and standard Windows PCs. You can also run OfficeGRID BLAST in a heavily Windows dominated environment with only one master/coordinating computer running Linux.
In a typically OfficeGRID setup - capable of running OfficeGRID BLAST - a stationary server is used as the master/coordinating computer and a dynamic set of desktop computers are acting as the workers that crunch data. The master/coordinating computer must have an OfficeGRID server appliation installed, while all other computers participating must have an OfficeGRID client application installed.
The OfficeGRID BLAST application is either installed on a network drive or distributed and installed automatically via OfficeGRID.
Handling Target Databases
When target databases are uploaded to the OfficeGRID, the target databases are automatically split into chunks of user defined size and distributed among all or some of the participating computers. The formatting process is done by calling the external program formatdb, which is created and maintained by NCBI. Because of this, the newest and most up-to-date version of formatdb can always be downloaded from the NCBI BLAST web site (www.ncbi.nlm.nih.gov/BLAST). I.e. if a new version of formatdb becomes available, it can, with no hassle, be installed into your existing OfficeGRID BLAST installation. The incorporation of the formatdb progam in OfficeGRID BLAST has also been optimized, thus resulting in significant time reductions when new target databases are introduced.
Querying the Target Databases
OfficeGRID BLAST searches are done using the newest and most up-to-date blastall program from NCBI. However one important feature has been added: User defined splitting of the input sequence.
OfficeGRID BLAST queries from one or more users are stored in a job queue, and handled independently.
OfficeGRID BLAST results are returned in the standard NCBI output format.
Scalability and Superlinear Speedup
Because OfficeGRID BLAST is built on OfficeGRID it inherits the useful scalability feature of OfficeGRID. I.e. the pool of computational power, which is available to OfficeGRID BLAST, can grow and shrink on demand without disturbing running BLAST queries. This means that it is possible to add more computational power when it is needed.
Tests of OfficeGRID BLAST has shown that the efficient memory utilization often results in superlinear speedup. This means that if one for example has 11 computers available, then it is very likely that the BLAST query will not only run 11 times as fast as on one computer, but perhaps more than 14 times as fast. This is can be interpreted as getting about 130% of the computational power out of the available computers.
OfficeGRID BLAST includes several tools, which can be used in the management of the target databases and also tools which can be used for management of the submitted BLAST queries. This set of management tools for submitted queries includes printing and dequeueing of submitted BLAST searches. These tools makes the daily management of an OfficeGRID BLAST installation very easy and flexible.
These tools makes the daily management of an OfficeGRID BLAST installation very easy and flexible.
OfficeGRID On-line Service
If you need extra BLAST processing or do not have the necessary computing resources for running BLAST processes in your company, please contact us. We can help you plan and implement your BLAST processing either in-house, externally or a combination of both.
|Contact MESH-Technologies for pricing and further information.|